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dbSNP Short Genetic Variations

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs12708965

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr16:56902407 (GRCh38.p12) Help

The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.

Alleles
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.03106 (7811/251468, GnomAD_exome)
T=0.03487 (4379/125568, TOPMED)
T=0.03057 (3710/121378, ExAC) (+ 9 more)
T=0.0501 (3940/78698, PAGE_STUDY)
T=0.0329 (1031/31368, GnomAD)
T=0.0345 (448/12996, GO-ESP)
T=0.052 (262/5008, 1000G)
T=0.013 (59/4480, Estonian)
T=0.011 (43/3854, ALSPAC)
T=0.010 (36/3708, TWINSUK)
T=0.04 (27/612, Vietnamese)
T=0.02 (10/600, NorthernSweden)
Clinical Significance
Reported in ClinVar
Gene : Consequence
SLC12A3 : Missense Variant
MIR6863 : 2KB Upstream Variant
Publications
2 citations
Genomic View
See rs on genome
Help

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements
Sequence name Change
GRCh38.p12 chr 16 NC_000016.10:g.56902407C>T
GRCh37.p13 chr 16 NC_000016.9:g.56936319C>T
SLC12A3 RefSeqGene NG_009386.1:g.42201C>T
Gene: SLC12A3, solute carrier family 12 member 3 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SLC12A3 transcript variant 2 NM_001126107.2:c.2779C>T R [CGT] > C [TGT] Coding Sequence Variant
solute carrier family 12 member 3 isoform 2 NP_001119579.2:p.Arg927Cys R (Arg) > C (Cys) Missense Variant
SLC12A3 transcript variant 1 NM_000339.3:c.2782C>T R [CGT] > C [TGT] Coding Sequence Variant
solute carrier family 12 member 3 isoform 1 NP_000330.3:p.Arg928Cys R (Arg) > C (Cys) Missense Variant
SLC12A3 transcript variant 3 NM_001126108.2:c.2755C>T R [CGT] > C [TGT] Coding Sequence Variant
solute carrier family 12 member 3 isoform 3 NP_001119580.2:p.Arg919Cys R (Arg) > C (Cys) Missense Variant
SLC12A3 transcript variant X1 XM_005256119.2:c.2752C>T R [CGT] > C [TGT] Coding Sequence Variant
solute carrier family 12 member 3 isoform X1 XP_005256176.1:p.Arg918Cys R (Arg) > C (Cys) Missense Variant
Gene: MIR6863, microRNA 6863 (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
MIR6863 transcript NR_106923.1:n. N/A Upstream Transcript Variant
Help

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Allele: T (allele ID: 341943 )
ClinVar Accession Disease Names Clinical Significance
RCV000405253.2 Familial hypokalemia-hypomagnesemia Benign-Likely-Benign
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Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

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Study Population Group Sample Size Ref Allele Alt Allele
gnomAD - Exomes Global Study-wide 251468 C=0.96894 T=0.03106
gnomAD - Exomes European Sub 135394 C=0.98388 T=0.01612
gnomAD - Exomes Asian Sub 49010 C=0.9587 T=0.0413
gnomAD - Exomes American Sub 34592 C=0.9557 T=0.0443
gnomAD - Exomes African Sub 16256 C=0.9261 T=0.0739
gnomAD - Exomes Ashkenazi Jewish Sub 10080 C=0.9330 T=0.0670
gnomAD - Exomes Other Sub 6136 C=0.968 T=0.032
TopMed Global Study-wide 125568 C=0.96513 T=0.03487
ExAC Global Study-wide 121378 C=0.96943 T=0.03057
ExAC Europe Sub 73336 C=0.9816 T=0.0184
ExAC Asian Sub 25164 C=0.9574 T=0.0426
ExAC American Sub 11574 C=0.9570 T=0.0430
ExAC African Sub 10398 C=0.9263 T=0.0737
ExAC Other Sub 906 C=0.97 T=0.03
The PAGE Study Global Study-wide 78698 C=0.9499 T=0.0501
The PAGE Study AfricanAmerican Sub 32516 C=0.9290 T=0.0710
The PAGE Study Mexican Sub 10810 C=0.9613 T=0.0387
The PAGE Study Asian Sub 8314 C=0.978 T=0.022
The PAGE Study PuertoRican Sub 7918 C=0.964 T=0.036
The PAGE Study NativeHawaiian Sub 4534 C=0.990 T=0.010
The PAGE Study Cuban Sub 4230 C=0.970 T=0.030
The PAGE Study Dominican Sub 3828 C=0.941 T=0.059
The PAGE Study CentralAmerican Sub 2450 C=0.945 T=0.055
The PAGE Study SouthAmerican Sub 1982 C=0.940 T=0.060
The PAGE Study NativeAmerican Sub 1260 C=0.957 T=0.043
The PAGE Study SouthAsian Sub 856 C=0.96 T=0.04
gnomAD - Genomes Global Study-wide 31368 C=0.9671 T=0.0329
gnomAD - Genomes European Sub 18884 C=0.9844 T=0.0156
gnomAD - Genomes African Sub 8700 C=0.928 T=0.072
gnomAD - Genomes East Asian Sub 1558 C=0.981 T=0.019
gnomAD - Genomes Other Sub 1088 C=0.970 T=0.030
gnomAD - Genomes American Sub 848 C=0.97 T=0.03
gnomAD - Genomes Ashkenazi Jewish Sub 290 C=0.93 T=0.07
GO Exome Sequencing Project Global Study-wide 12996 C=0.9655 T=0.0345
GO Exome Sequencing Project European American Sub 8600 C=0.983 T=0.017
GO Exome Sequencing Project African American Sub 4396 C=0.932 T=0.068
1000Genomes Global Study-wide 5008 C=0.948 T=0.052
1000Genomes African Sub 1322 C=0.915 T=0.085
1000Genomes East Asian Sub 1008 C=0.974 T=0.026
1000Genomes Europe Sub 1006 C=0.984 T=0.016
1000Genomes South Asian Sub 978 C=0.93 T=0.07
1000Genomes American Sub 694 C=0.95 T=0.05
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.987 T=0.013
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.989 T=0.011
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.990 T=0.010
A Vietnamese Genetic Variation Database Global Study-wide 612 C=0.96 T=0.04
Northern Sweden ACPOP Study-wide 600 C=0.98 T=0.02
Help

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement C= T Note
GRCh38.p12 chr 16 NC_000016.10:g.56902407= NC_000016.10:g.56902407C>T
GRCh37.p13 chr 16 NC_000016.9:g.56936319= NC_000016.9:g.56936319C>T
SLC12A3 RefSeqGene NG_009386.1:g.42201= NG_009386.1:g.42201C>T
SLC12A3 transcript variant 1 NM_000339.3:c.2782= NM_000339.3:c.2782C>T
SLC12A3 transcript variant 1 NM_000339.2:c.2782= NM_000339.2:c.2782C>T
SLC12A3 transcript variant 2 NM_001126107.2:c.2779= NM_001126107.2:c.2779C>T
SLC12A3 transcript variant 2 NM_001126107.1:c.2779= NM_001126107.1:c.2779C>T
SLC12A3 transcript variant 3 NM_001126108.2:c.2755= NM_001126108.2:c.2755C>T
SLC12A3 transcript variant 3 NM_001126108.1:c.2755= NM_001126108.1:c.2755C>T
SLC12A3 transcript variant X1 XM_005256119.2:c.2752= XM_005256119.2:c.2752C>T
SLC12A3 transcript variant X1 XM_005256119.1:c.2752= XM_005256119.1:c.2752C>T
solute carrier family 12 member 3 isoform 1 NP_000330.3:p.Arg928= NP_000330.3:p.Arg928Cys
solute carrier family 12 member 3 isoform 2 NP_001119579.2:p.Arg927= NP_001119579.2:p.Arg927Cys
solute carrier family 12 member 3 isoform 3 NP_001119580.2:p.Arg919= NP_001119580.2:p.Arg919Cys
solute carrier family 12 member 3 isoform X1 XP_005256176.1:p.Arg918= XP_005256176.1:p.Arg918Cys
Help

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

97 SubSNP, 12 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 SSAHASNP ss21352734 Apr 05, 2004 (121)
2 IMCJ-GDT ss22887793 Apr 05, 2004 (121)
3 PERLEGEN ss23417545 Sep 20, 2004 (123)
4 ABI ss43969623 Mar 13, 2006 (126)
5 APPLERA_GI ss48422082 Mar 13, 2006 (126)
6 UCSF_HG ss49783642 Mar 13, 2006 (126)
7 ILLUMINA ss67359001 Nov 29, 2006 (127)
8 PERLEGEN ss69345379 May 16, 2007 (127)
9 PHARMGKB_PCE ss69368188 May 16, 2007 (127)
10 ILLUMINA ss71125189 May 16, 2007 (127)
11 ILLUMINA ss75390010 Dec 06, 2007 (129)
12 HUMANGENOME_JCVI ss96685207 Feb 05, 2009 (130)
13 ENSEMBL ss136725099 Dec 01, 2009 (131)
14 ILLUMINA ss153273251 Dec 01, 2009 (131)
15 ILLUMINA ss159232440 Dec 01, 2009 (131)
16 SEATTLESEQ ss159732951 Dec 01, 2009 (131)
17 ILLUMINA ss160296209 Dec 01, 2009 (131)
18 COMPLETE_GENOMICS ss171290669 Jul 04, 2010 (132)
19 ILLUMINA ss172229531 Jul 04, 2010 (132)
20 BUSHMAN ss201740078 Jul 04, 2010 (132)
21 1000GENOMES ss211716015 Jul 14, 2010 (132)
22 1000GENOMES ss227261701 Jul 14, 2010 (132)
23 1000GENOMES ss243376350 Jul 15, 2010 (132)
24 ILLUMINA ss244277309 Jul 04, 2010 (132)
25 PJP ss291850327 May 09, 2011 (134)
26 NHLBI-ESP ss342429301 May 09, 2011 (134)
27 ILLUMINA ss479494044 May 04, 2012 (137)
28 ILLUMINA ss479810304 May 04, 2012 (137)
29 ILLUMINA ss479817380 May 04, 2012 (137)
30 ILLUMINA ss480401621 Sep 08, 2015 (146)
31 ILLUMINA ss483521447 May 04, 2012 (137)
32 ILLUMINA ss484703642 May 04, 2012 (137)
33 1000GENOMES ss491103753 May 04, 2012 (137)
34 EXOME_CHIP ss491508728 May 04, 2012 (137)
35 CLINSEQ_SNP ss491719185 May 04, 2012 (137)
36 ILLUMINA ss533035385 Sep 08, 2015 (146)
37 SSMP ss660695777 Apr 25, 2013 (138)
38 ILLUMINA ss779163908 Sep 08, 2015 (146)
39 ILLUMINA ss780995372 Sep 08, 2015 (146)
40 ILLUMINA ss782798588 Sep 08, 2015 (146)
41 ILLUMINA ss832051526 Sep 08, 2015 (146)
42 ILLUMINA ss832744780 Jul 13, 2019 (153)
43 ILLUMINA ss834628986 Sep 08, 2015 (146)
44 JMKIDD_LAB ss974495083 Aug 21, 2014 (142)
45 EVA-GONL ss992525542 Aug 21, 2014 (142)
46 JMKIDD_LAB ss1067561866 Aug 21, 2014 (142)
47 JMKIDD_LAB ss1080650272 Aug 21, 2014 (142)
48 1000GENOMES ss1356387666 Aug 21, 2014 (142)
49 EVA_FINRISK ss1584100133 Apr 01, 2015 (144)
50 EVA_UK10K_ALSPAC ss1634498357 Apr 01, 2015 (144)
51 EVA_UK10K_TWINSUK ss1677492390 Apr 01, 2015 (144)
52 EVA_EXAC ss1692313252 Apr 01, 2015 (144)
53 EVA_DECODE ss1696560091 Apr 01, 2015 (144)
54 EVA_MGP ss1711430451 Apr 01, 2015 (144)
55 EVA_SVP ss1713541914 Apr 01, 2015 (144)
56 ILLUMINA ss1752195901 Sep 08, 2015 (146)
57 WEILL_CORNELL_DGM ss1935961763 Feb 12, 2016 (147)
58 ILLUMINA ss1959681807 Feb 12, 2016 (147)
59 GENOMED ss1968270242 Jul 19, 2016 (147)
60 JJLAB ss2028764284 Sep 14, 2016 (149)
61 USC_VALOUEV ss2157200803 Dec 20, 2016 (150)
62 HUMAN_LONGEVITY ss2212442583 Dec 20, 2016 (150)
63 ILLUMINA ss2633322603 Nov 08, 2017 (151)
64 ILLUMINA ss2633322604 Nov 08, 2017 (151)
65 GRF ss2701725458 Nov 08, 2017 (151)
66 GNOMAD ss2742002156 Nov 08, 2017 (151)
67 GNOMAD ss2749548196 Nov 08, 2017 (151)
68 GNOMAD ss2943409328 Nov 08, 2017 (151)
69 AFFY ss2985069687 Nov 08, 2017 (151)
70 AFFY ss2985705740 Nov 08, 2017 (151)
71 SWEGEN ss3014570276 Nov 08, 2017 (151)
72 ILLUMINA ss3021709679 Nov 08, 2017 (151)
73 TOPMED ss3247437809 Nov 08, 2017 (151)
74 ILLUMINA ss3627531563 Oct 12, 2018 (152)
75 ILLUMINA ss3631308778 Oct 12, 2018 (152)
76 ILLUMINA ss3633121927 Oct 12, 2018 (152)
77 ILLUMINA ss3633828056 Oct 12, 2018 (152)
78 ILLUMINA ss3634643645 Oct 12, 2018 (152)
79 ILLUMINA ss3635516336 Oct 12, 2018 (152)
80 ILLUMINA ss3636335131 Oct 12, 2018 (152)
81 ILLUMINA ss3637267773 Oct 12, 2018 (152)
82 ILLUMINA ss3638127174 Oct 12, 2018 (152)
83 ILLUMINA ss3640350965 Oct 12, 2018 (152)
84 ILLUMINA ss3643108200 Oct 12, 2018 (152)
85 OMUKHERJEE_ADBS ss3646494915 Oct 12, 2018 (152)
86 URBANLAB ss3650517913 Oct 12, 2018 (152)
87 ILLUMINA ss3652118657 Oct 12, 2018 (152)
88 ILLUMINA ss3653841646 Oct 12, 2018 (152)
89 EGCUT_WGS ss3681545864 Jul 13, 2019 (153)
90 EVA_DECODE ss3699332642 Jul 13, 2019 (153)
91 ILLUMINA ss3725565071 Jul 13, 2019 (153)
92 ACPOP ss3741541742 Jul 13, 2019 (153)
93 ILLUMINA ss3744944071 Jul 13, 2019 (153)
94 EVA ss3753981851 Jul 13, 2019 (153)
95 PAGE_CC ss3771881799 Jul 13, 2019 (153)
96 ILLUMINA ss3772442332 Jul 13, 2019 (153)
97 KHV_HUMAN_GENOMES ss3819268565 Jul 13, 2019 (153)
98 1000Genomes NC_000016.9 - 56936319 Oct 12, 2018 (152)
99 The Avon Longitudinal Study of Parents and Children NC_000016.9 - 56936319 Oct 12, 2018 (152)
100 Genetic variation in the Estonian population NC_000016.9 - 56936319 Oct 12, 2018 (152)
101 ExAC NC_000016.9 - 56936319 Oct 12, 2018 (152)
102 gnomAD - Genomes NC_000016.9 - 56936319 Jul 13, 2019 (153)
103 gnomAD - Exomes NC_000016.9 - 56936319 Jul 13, 2019 (153)
104 GO Exome Sequencing Project NC_000016.9 - 56936319 Oct 12, 2018 (152)
105 Northern Sweden NC_000016.9 - 56936319 Jul 13, 2019 (153)
106 The PAGE Study NC_000016.10 - 56902407 Jul 13, 2019 (153)
107 TopMed NC_000016.10 - 56902407 Oct 12, 2018 (152)
108 UK 10K study - Twins NC_000016.9 - 56936319 Oct 12, 2018 (152)
109 A Vietnamese Genetic Variation Database NC_000016.9 - 56936319 Jul 13, 2019 (153)
110 ClinVar RCV000405253.2 Oct 12, 2018 (152)
Help

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss171290669, ss201740078, ss211716015, ss291850327, ss479810304, ss483521447, ss491719185, ss1696560091, ss1713541914, ss3643108200 NC_000016.8:55493819:C:T NC_000016.10:56902406:C:T (self)
69554622, 38581684, 27284112, 2721800, 189777388, 11282254, 1475344, 14826607, 38581684, 8559941, ss227261701, ss243376350, ss342429301, ss479494044, ss479817380, ss480401621, ss484703642, ss491103753, ss491508728, ss533035385, ss660695777, ss779163908, ss780995372, ss782798588, ss832051526, ss832744780, ss834628986, ss974495083, ss992525542, ss1067561866, ss1080650272, ss1356387666, ss1584100133, ss1634498357, ss1677492390, ss1692313252, ss1711430451, ss1752195901, ss1935961763, ss1959681807, ss1968270242, ss2028764284, ss2157200803, ss2633322603, ss2633322604, ss2701725458, ss2742002156, ss2749548196, ss2943409328, ss2985069687, ss2985705740, ss3014570276, ss3021709679, ss3627531563, ss3631308778, ss3633121927, ss3633828056, ss3634643645, ss3635516336, ss3636335131, ss3637267773, ss3638127174, ss3640350965, ss3646494915, ss3652118657, ss3653841646, ss3681545864, ss3741541742, ss3744944071, ss3753981851, ss3772442332 NC_000016.9:56936318:C:T NC_000016.10:56902406:C:T (self)
RCV000405253.2, 1103268, 144951939, ss2212442583, ss3247437809, ss3650517913, ss3699332642, ss3725565071, ss3771881799, ss3819268565 NC_000016.10:56902406:C:T NC_000016.10:56902406:C:T (self)
ss21352734 NT_010498.14:5657031:C:T NC_000016.10:56902406:C:T (self)
ss22887793, ss23417545, ss43969623, ss48422082, ss49783642, ss67359001, ss69345379, ss69368188, ss71125189, ss75390010, ss96685207, ss136725099, ss153273251, ss159232440, ss159732951, ss160296209, ss172229531, ss244277309 NT_010498.15:10550517:C:T NC_000016.10:56902406:C:T (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

2 citations for rs12708965
PMID Title Author Year Journal
9734597 Novel mutations in the thiazide-sensitive NaCl cotransporter gene in patients with Gitelman syndrome with predominant localization to the C-terminal domain. Lemmink HH et al. 1998 Kidney international
21415153 Spectrum of mutations in Gitelman syndrome. Vargas-Poussou R et al. 2011 Journal of the American Society of Nephrology

Genomic regions, transcripts, and products
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NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Software version is: 2.0.1.post270+ab078da